PHI-base: the pathogen–host interactions database
Martin Urban,Alayne Cuzick,James Seager,Valerie Wood,Kim Rutherford,Shilpa Yagwakote Venkatesh,Nishadi De Silva,Manuel Carbajo Martinez,Helder Pedro,Andrew D. Yates,Keywan Hassani-Pak,Kim E. Hammond-Kosack +11 more
272
TL;DR: The increased data content of PHI-base is described, plus new database features and further integration with complementary databases are described, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release.
read more
Abstract: The pathogen-host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.
Beatrice Amos,Cristina Aurrecoechea,Matthieu Barba,Ana Barreto,Evelina Y. Basenko,Wojciech Bażant,Robert Belnap,Ann Sizemore Blevins,Ulrike Böhme,John Brestelli,Brian P. Brunk,Mark X. Caddick,Danielle Callan,Lahcen I. Campbell,Mikkel B. Christensen,George K. Christophides,Kathryn Crouch,Kristina Davis,Jeremy D. DeBarry,Ryan Doherty,Yikun Duan,Michael J. Dunn,Dave Falke,Steve Fisher,Paul Flicek,Brett Fox,Bindu Gajria,Gloria I. Giraldo-Calderón,Gloria I. Giraldo-Calderón,Omar S. Harb,Elizabeth Harper,Christiane Hertz-Fowler,Mark J Hickman,Connor Howington,Sufen Hu,Jay C. Humphrey,John Iodice,Andrew M. Jones,John Judkins,Sarah A. Kelly,Jessica C. Kissinger,Dae Kun Kwon,Kristopher Lamoureux,Daniel Lawson,Wei Li,Kallie Lies,Disha Lodha,Jamie Long,Robert M. MacCallum,Gareth Maslen,Mary Ann McDowell,Jaroslaw Nabrzyski,David S. Roos,Samuel S. C. Rund,Stephanie Wever Schulman,Achchuthan Shanmugasundram,Vasily Sitnik,Drew Spruill,David Starns,Christian J. Stoeckert,Sheena Shah Tomko,Haiming Wang,Susanne Warrenfeltz,Robert Wieck,Paul A Wilkinson,Lin Xu,Jie Zheng +66 more
TL;DR: The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPath database as mentioned in this paper.
384
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.
Andrew D. Yates,James E. Allen,Ridwan M Amode,Andrey G Azov,Matthieu Barba,Andrés Becerra,Jyothish Bhai,Lahcen I. Campbell,Manuel Carbajo Martinez,Marc Chakiachvili,Kapeel Chougule,Mikkel B. Christensen,Bruno Contreras-Moreira,Alayne Cuzick,Luca Da Rin Fioretto,Paul Davis,Nishadi De Silva,Stavros Diamantakis,Sarah Dyer,Justin Elser,Carla Valeria Filippi,Carla Valeria Filippi,Carla Valeria Filippi,Astrid Gall,Dionysios Grigoriadis,Cristina Guijarro-Clarke,Parul Gupta,Kim E. Hammond-Kosack,Kevin L. Howe,Pankaj Jaiswal,Vinay Kaikala,Vivek Kumar,Sunita Kumari,Nick Langridge,Tuan Le,Manuel Luypaert,Gareth Maslen,Thomas Maurel,Benjamin Moore,Matthieu Muffato,Aleena Mushtaq,Guy Naamati,Sushma Naithani,Andrew Olson,Anne Parker,Michael Paulini,Helder Pedro,Emily Perry,Justin Preece,Mark Quinton-Tulloch,Faye H. Rodgers,Marc Rosello,Magali Ruffier,James Seager,Vasily Sitnik,Michal Szpak,John Tate,Marcela K. Tello-Ruiz,Stephen J. Trevanion,Martin Urban,Doreen Ware,Doreen Ware,Sharon Wei,Gary Williams,Andrea Winterbottom,Magdalena Zarowiecki,Robert D. Finn,Paul Flicek +67 more
TL;DR: Ensembl Genomes as discussed by the authors provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensemblgenomes.org).
256
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.
Martin Urban,Alayne Cuzick,James Seager,Valerie Wood,Kim Rutherford,Shilpa Yagwakote Venkatesh,Jashobanta Sahu,S Vijaylakshmi Iyer,Lokanath Khamari,Nishadi De Silva,Manuel Carbajo Martinez,Helder Pedro,Andrew D. Yates,Kim E. Hammond-Kosack +13 more
TL;DR: The Pathogen-Host Interactions Database (PHI-base) as discussed by the authors has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and or fungal hosts.
95
The 27th annual Nucleic Acids Research database issue and molecular biology database collection
TL;DR: This issue contains three breakthrough articles: AntiBodies Chemically Defined curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools.
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection.
Amelia E. Barber,Tongta Sae-Ong,Kang Kang,Bastian Seelbinder,Jun Li,Grit Walther,Gianni Panagiotou,Gianni Panagiotou,Oliver Kurzai,Oliver Kurzai +9 more
TL;DR: In this paper, the pan-genome of Aspergillus fumigatus is defined using a collection of 300 globally sampled genomes (83 clinical and 217 environmental isolates).
76
References
The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan-Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more
TL;DR: The FAIR Data Principles as mentioned in this paper are a set of data reuse principles that focus on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals.
The plant immune system
TL;DR: A detailed understanding of plant immune function will underpin crop improvement for food, fibre and biofuels production and provide extraordinary insights into molecular recognition, cell biology and evolution across biological kingdoms.
12.3K
High-throughput functional annotation and data mining with the Blast2GO suite.
Stefan Götz,Juan M. García-Gómez,Javier Terol,Tim D. Williams,Shivashankar H. Nagaraj,María José Nueda,Montserrat Robles,Manuel Talon,Joaquín Dopazo,Ana Conesa +9 more
TL;DR: The Blast2GO framework is used to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.
4K
Hidden Killers: Human Fungal Infections
Gordon D. Brown,David W. Denning,Neil A. R. Gow,Stuart M. Levitz,Mihai G. Netea,Theodore C. White +5 more
TL;DR: The importance of fungi as human pathogens is highlighted and the challenges the authors face in combating the devastating invasive infections caused by these microorganisms are discussed, in particular in immunocompromised individuals.